Not that Bethany shows any sort of reluctance in killing Templars. She pretty much agrees with Anders' views but she doesn't want to employ violence. She is nice like that. (refer to party banter between the two). She wants to be free and not be bound for an accident of birth.
Circle mage Bethany talks about how she originally thought the Maker wanted mages locked up in the Circle Towers, and how she realizes mages should be free, in the pro-mage scene at the Gallows.
No one is claiming anything but there is no proof whatsoever that there were children inside. The exact game scene shows around 10 people, Elthina and a couple of priests and templars. You can claim there were more but cannot claim they were children.
I believe there was debate about whether anyone besides the clergy and the templars would be present during the explosion, since the Kirkwall Chantry was apparently closed to the public at night, given how Hawke fights templars and Petrice's zealots there during Acts I and II.
Anders is product of chantry. His own parents hated him because of chantry propaganda and he was in solitude of circle prison for many years, lost people he cared about etc.... All events of Anders' life which stem from chantry affected his whole personality. Their own hate and oppression exploded in their own face, literally in form of Anders. Maybe that particular chantry didn't deserve it, the chantry in general deserved it and then some.
Anders is religiously Andrastian, despite his disagreement about the Chantry controlled Circles, which is where most of his frustration comes from, especially when he was taken away. He confides in Hawke about growing up in the Circle Tower, his relationship with Karl, and about the suicides that took place who were despondent about life in the Circle.